메뉴 건너뛰기




Volumn 2, Issue 1, 2014, Pages

Caught in the middle with multiple displacement amplification: The myth of pooling for avoiding multiple displacement amplification bias in a metagenome

Author keywords

DNA library construction; Metagenomics; Microbial ecology; Multiple displacement amplification; PacBio SMRT sequencing

Indexed keywords

ARTICLE; BACTERIOPHAGE; DNA EXTRACTION; DNA LIBRARY; GENE AMPLIFICATION; GENE SEQUENCE; METAGENOME; MICROBIAL COMMUNITY; MULTIPLE DISPLACEMENT AMPLIFICATION; NONHUMAN; PRIORITY JOURNAL; PYROSEQUENCING; VIRUS GENOME;

EID: 84926418348     PISSN: None     EISSN: 20492618     Source Type: Journal    
DOI: 10.1186/2049-2618-2-3     Document Type: Article
Times cited : (84)

References (43)
  • 1
    • 84865720549 scopus 로고    scopus 로고
    • Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method
    • 3466414, 22713159
    • Duhaime MB, Deng L, Poulos BT, Sullivan MB. Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method. Environ Microbiol 2012, 14:2526-2537. 10.1111/j.1462-2920.2012.02791.x, 3466414, 22713159.
    • (2012) Environ Microbiol , vol.14 , pp. 2526-2537
    • Duhaime, M.B.1    Deng, L.2    Poulos, B.T.3    Sullivan, M.B.4
  • 2
    • 83055180102 scopus 로고    scopus 로고
    • Evaluation of a transposase protocol for rapid generation of shotgun high-throughput sequencing libraries from nanogram quantities of DNA
    • 3209006, 21948828
    • Marine R, Polson SW, Ravel J, Hatfull G, Russell D, Sullivan M, Syed F, Dumas M, Wommack KE. Evaluation of a transposase protocol for rapid generation of shotgun high-throughput sequencing libraries from nanogram quantities of DNA. Appl Environ Microbiol 2011, 77:8071-8079. 10.1128/AEM.05610-11, 3209006, 21948828.
    • (2011) Appl Environ Microbiol , vol.77 , pp. 8071-8079
    • Marine, R.1    Polson, S.W.2    Ravel, J.3    Hatfull, G.4    Russell, D.5    Sullivan, M.6    Syed, F.7    Dumas, M.8    Wommack, K.E.9
  • 5
    • 64749109065 scopus 로고    scopus 로고
    • Laboratory procedures to generate viral metagenomes
    • 19300441
    • Thurber RV, Haynes M, Breitbart M, Wegley L, Rohwer F. Laboratory procedures to generate viral metagenomes. Nat Protoc 2009, 4:470-483. 10.1038/nprot.2009.10, 19300441.
    • (2009) Nat Protoc , vol.4 , pp. 470-483
    • Thurber, R.V.1    Haynes, M.2    Breitbart, M.3    Wegley, L.4    Rohwer, F.5
  • 6
    • 0242475336 scopus 로고    scopus 로고
    • Whole genome amplification: abundant supplies of DNA from precious samples or clinical specimens
    • 14624861
    • Lasken RS, Egholm M. Whole genome amplification: abundant supplies of DNA from precious samples or clinical specimens. Trends Biotechnol 2003, 21:531-535. 10.1016/j.tibtech.2003.09.010, 14624861.
    • (2003) Trends Biotechnol , vol.21 , pp. 531-535
    • Lasken, R.S.1    Egholm, M.2
  • 7
    • 40249095175 scopus 로고    scopus 로고
    • Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology
    • 18256705
    • Binga EK, Lasken RS, Neufeld JD. Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology. ISME J 2008, 2:233-241. 10.1038/ismej.2008.10, 18256705.
    • (2008) ISME J , vol.2 , pp. 233-241
    • Binga, E.K.1    Lasken, R.S.2    Neufeld, J.D.3
  • 8
    • 78751575713 scopus 로고    scopus 로고
    • Unraveling the viral tapestry (from inside the capsid out)
    • 3105704, 20555364
    • Polson SW, Wilhelm SW, Wommack KE. Unraveling the viral tapestry (from inside the capsid out). ISME J 2011, 5:165-168. 10.1038/ismej.2010.81, 3105704, 20555364.
    • (2011) ISME J , vol.5 , pp. 165-168
    • Polson, S.W.1    Wilhelm, S.W.2    Wommack, K.E.3
  • 9
    • 78649707158 scopus 로고    scopus 로고
    • Multiple displacement amplification compromises quantitative analysis of metagenomes
    • 21116242
    • Yilmaz S, Allgaier M, Hugenholtz P. Multiple displacement amplification compromises quantitative analysis of metagenomes. Nat Methods 2010, 7:943-944. 10.1038/nmeth1210-943, 21116242.
    • (2010) Nat Methods , vol.7 , pp. 943-944
    • Yilmaz, S.1    Allgaier, M.2    Hugenholtz, P.3
  • 11
    • 79960082882 scopus 로고    scopus 로고
    • Microarray-based evaluation of whole-community genome DNA amplification methods
    • 3131669, 21498751
    • Wang J, Van Nostrand JD, Wu L, He Z, Li G, Zhou J. Microarray-based evaluation of whole-community genome DNA amplification methods. Appl Environ Microbiol 2011, 77:4241-4245. 10.1128/AEM.01834-10, 3131669, 21498751.
    • (2011) Appl Environ Microbiol , vol.77 , pp. 4241-4245
    • Wang, J.1    Van Nostrand, J.D.2    Wu, L.3    He, Z.4    Li, G.5    Zhou, J.6
  • 14
    • 40149098974 scopus 로고    scopus 로고
    • Microbial ecology of four coral atolls in the Northern Line Islands
    • 2253183, 18301735
    • Dinsdale EA, Pantos O, Smriga S, Edwards RA. Microbial ecology of four coral atolls in the Northern Line Islands. PLoS One 2008, 3:e1584. 10.1371/journal.pone.0001584, 2253183, 18301735.
    • (2008) PLoS One , vol.3 , pp. e1584
    • Dinsdale, E.A.1    Pantos, O.2    Smriga, S.3    Edwards, R.A.4
  • 16
    • 84866175103 scopus 로고    scopus 로고
    • Temporal dynamics and decay of putatively allochthonous and autochthonous viral genotypes in contrasting freshwater lakes
    • 3426699, 22773646
    • Hewson I, Barbosa JG, Brown JM, Donelan RP, Eaglesham JB, Eggleston EM, Labarre BA. Temporal dynamics and decay of putatively allochthonous and autochthonous viral genotypes in contrasting freshwater lakes. Appl Environ Microbiol 2012, 78:6583-6591. 10.1128/AEM.01705-12, 3426699, 22773646.
    • (2012) Appl Environ Microbiol , vol.78 , pp. 6583-6591
    • Hewson, I.1    Barbosa, J.G.2    Brown, J.M.3    Donelan, R.P.4    Eaglesham, J.B.5    Eggleston, E.M.6    Labarre, B.A.7
  • 17
    • 70350545933 scopus 로고    scopus 로고
    • Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals
    • 2756586, 19816605
    • Willner D, Furlan M, Haynes M, Schmieder R, Angly FE, Silva J, Tammadoni S, Nosrat B, Conrad D, Rohwer F. Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals. PLoS One 2009, 4:e7370. 10.1371/journal.pone.0007370, 2756586, 19816605.
    • (2009) PLoS One , vol.4 , pp. e7370
    • Willner, D.1    Furlan, M.2    Haynes, M.3    Schmieder, R.4    Angly, F.E.5    Silva, J.6    Tammadoni, S.7    Nosrat, B.8    Conrad, D.9    Rohwer, F.10
  • 18
    • 68549104404 scopus 로고    scopus 로고
    • The sequence alignment/Map format and SAMtools
    • 2723002, 19505943, 1000 Genome Project Data Processing Subgroup
    • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, . 1000 Genome Project Data Processing Subgroup The sequence alignment/Map format and SAMtools. Bioinformatics 2009, 25:2078-2079. 10.1093/bioinformatics/btp352, 2723002, 19505943, 1000 Genome Project Data Processing Subgroup.
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1    Handsaker, B.2    Wysoker, A.3    Fennell, T.4    Ruan, J.5    Homer, N.6    Marth, G.7    Abecasis, G.8    Durbin, R.9
  • 19
    • 80055091440 scopus 로고    scopus 로고
    • R Project for Statistical Computing
    • R Project for Statistical Computing. [http://www.r-project.org/].
  • 20
    • 84938484275 scopus 로고    scopus 로고
    • Pacific biosciences technical notes, microbial assembly experimental design
    • Pacific biosciences technical notes, microbial assembly experimental design. [http://www.pacificbiosciences.com/pdf/TechnicalNote_Experimental_Design_for_Microbial_Assembly.pdf].
  • 21
    • 16444364507 scopus 로고    scopus 로고
    • Effects of electron-beam irradiation on whole genome amplification
    • Bergen AW. Effects of electron-beam irradiation on whole genome amplification. Cancer Epidem Biomar 2005, 14:1016-1019.
    • (2005) Cancer Epidem Biomar , vol.14 , pp. 1016-1019
    • Bergen, A.W.1
  • 23
    • 57149097677 scopus 로고    scopus 로고
    • Successful amplification of degraded DNA for use with high-throughput SNP genotyping platforms
    • 18551557
    • Mead S, Poulter M, Beck J, Uphill J, Jones C, Ang CE, Mein CA, Collinge J. Successful amplification of degraded DNA for use with high-throughput SNP genotyping platforms. Hum Mutat 2008, 29:1452-1458. 10.1002/humu.20782, 18551557.
    • (2008) Hum Mutat , vol.29 , pp. 1452-1458
    • Mead, S.1    Poulter, M.2    Beck, J.3    Uphill, J.4    Jones, C.5    Ang, C.E.6    Mein, C.A.7    Collinge, J.8
  • 25
    • 77955883388 scopus 로고    scopus 로고
    • Biases in Illumina transcriptome sequencing caused by random hexamer priming
    • 2896536, 20395217
    • Hansen KD, Brenner SE, Dudoit S. Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res 2010, 38:e131. 10.1093/nar/gkq224, 2896536, 20395217.
    • (2010) Nucleic Acids Res , vol.38 , pp. e131
    • Hansen, K.D.1    Brenner, S.E.2    Dudoit, S.3
  • 26
    • 25644456831 scopus 로고    scopus 로고
    • Ligation overcomes terminal underrepresentation in multiple displacement amplification of linear DNA
    • 16116788
    • Panelli S, Damiani G, Espen L, Sgaramella V. Ligation overcomes terminal underrepresentation in multiple displacement amplification of linear DNA. Biotechniques 2005, 39:174-180. 10.2144/05392BM03, 16116788.
    • (2005) Biotechniques , vol.39 , pp. 174-180
    • Panelli, S.1    Damiani, G.2    Espen, L.3    Sgaramella, V.4
  • 27
    • 14944380100 scopus 로고    scopus 로고
    • Genome-wide single-nucleotide polymorphism arrays demonstrate high fidelity of multiple displacement-based whole-genome amplification
    • 15690424
    • Tzvetkov MV, Becker C, Kulle B, Nürnberg P, Brockmöller J, Wojnowski L. Genome-wide single-nucleotide polymorphism arrays demonstrate high fidelity of multiple displacement-based whole-genome amplification. Electrophoresis 2005, 26:710-715. 10.1002/elps.200410121, 15690424.
    • (2005) Electrophoresis , vol.26 , pp. 710-715
    • Tzvetkov, M.V.1    Becker, C.2    Kulle, B.3    Nürnberg, P.4    Brockmöller, J.5    Wojnowski, L.6
  • 28
    • 84455173447 scopus 로고    scopus 로고
    • Genomics of bacterial and archaeal viruses: dynamics within the prokaryotic virosphere
    • 3232739, 22126996
    • Krupovic M, Prangishvili D, Hendrix RW, Bamford DH. Genomics of bacterial and archaeal viruses: dynamics within the prokaryotic virosphere. Microbiol Mol Biol Rev 2011, 75:610-635. 10.1128/MMBR.00011-11, 3232739, 22126996.
    • (2011) Microbiol Mol Biol Rev , vol.75 , pp. 610-635
    • Krupovic, M.1    Prangishvili, D.2    Hendrix, R.W.3    Bamford, D.H.4
  • 29
    • 0035153828 scopus 로고    scopus 로고
    • Comparative phage genomics and the evolution of Siphoviridae: insights from dairy phages
    • 11136444
    • Brüssow H, Desiere F. Comparative phage genomics and the evolution of Siphoviridae: insights from dairy phages. Mol Microbiol 2001, 39:213-222. 10.1046/j.1365-2958.2001.02228.x, 11136444.
    • (2001) Mol Microbiol , vol.39 , pp. 213-222
    • Brüssow, H.1    Desiere, F.2
  • 33
    • 83155190998 scopus 로고    scopus 로고
    • Amplification methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses
    • 3209148, 21926223
    • Kim KH, Bae JW. Amplification methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses. Appl Environ Microbiol 2011, 77:7663-7668. 10.1128/AEM.00289-11, 3209148, 21926223.
    • (2011) Appl Environ Microbiol , vol.77 , pp. 7663-7668
    • Kim, K.H.1    Bae, J.W.2
  • 36
    • 33748591589 scopus 로고    scopus 로고
    • Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing
    • 1560136, 16928277
    • Pinard R, de Winter A, Sarkis GJ, Gerstein MB, Tartaro KR, Plant RN, Egholm M, Rothberg JM, Leamon JH. Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing. BMC Genomics 2006, 7:216. 10.1186/1471-2164-7-216, 1560136, 16928277.
    • (2006) BMC Genomics , vol.7 , pp. 216
    • Pinard, R.1    de Winter, A.2    Sarkis, G.J.3    Gerstein, M.B.4    Tartaro, K.R.5    Plant, R.N.6    Egholm, M.7    Rothberg, J.M.8    Leamon, J.H.9
  • 37
    • 63949083912 scopus 로고    scopus 로고
    • Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G + C)-biased genomes
    • 2664327, 19287394
    • Kozarewa I, Ning Z, Quail MA, Sanders MJ, Berriman M, Turner DJ. Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G + C)-biased genomes. Nat Methods 2009, 6:291-295. 10.1038/nmeth.1311, 2664327, 19287394.
    • (2009) Nat Methods , vol.6 , pp. 291-295
    • Kozarewa, I.1    Ning, Z.2    Quail, M.A.3    Sanders, M.J.4    Berriman, M.5    Turner, D.J.6
  • 38
    • 84871352308 scopus 로고    scopus 로고
    • Direct sequencing of small genomes on the pacific biosciences RS without library preparation
    • 3808810, 23227987
    • Coupland P, Chandra T, Quail M, Reik W, Swerdlow H. Direct sequencing of small genomes on the pacific biosciences RS without library preparation. Biotechniques 2012, 53:365-372. 3808810, 23227987.
    • (2012) Biotechniques , vol.53 , pp. 365-372
    • Coupland, P.1    Chandra, T.2    Quail, M.3    Reik, W.4    Swerdlow, H.5
  • 42
    • 83055177100 scopus 로고    scopus 로고
    • Diversity and abundance of single-stranded DNA viruses in human feces
    • 3208976, 21948823
    • Kim M, Park E, Roh SW, Bae J. Diversity and abundance of single-stranded DNA viruses in human feces. Appl Environ Microbiol 2011, 77:8062-8070. 10.1128/AEM.06331-11, 3208976, 21948823.
    • (2011) Appl Environ Microbiol , vol.77 , pp. 8062-8070
    • Kim, M.1    Park, E.2    Roh, S.W.3    Bae, J.4
  • 43
    • 70350482684 scopus 로고    scopus 로고
    • Metagenomic analysis of viruses in reclaimed water
    • 19555373
    • Rosario K, Nilsson C, Lim YW, Ruan Y, Breitbart M. Metagenomic analysis of viruses in reclaimed water. Environ Microbiol 2009, 11:2806-2820. 10.1111/j.1462-2920.2009.01964.x, 19555373.
    • (2009) Environ Microbiol , vol.11 , pp. 2806-2820
    • Rosario, K.1    Nilsson, C.2    Lim, Y.W.3    Ruan, Y.4    Breitbart, M.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.